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Escherichia coli strain EC_80 EC80_77, whole genome shotgun sequence

NCBI Reference Sequence: NZ_VDBG01000077.1

FASTA Graphics 

LOCUS       NZ_VDBG01000077         7483 bp    DNA     linear   CON 23-NOV-2024
DEFINITION  Escherichia coli strain EC_80 EC80_77, whole genome shotgun
            sequence.
ACCESSION   NZ_VDBG01000077 NZ_VDBG01000000
VERSION     NZ_VDBG01000077.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11855603
            Assembly: GCF_019583735.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 7483)
  AUTHORS   Ikhimiukor,O., Vollmers,J., Adeleke,R.A., Kaster,A.-K.,
            Mueller,J.A. and Adelowo,O.
  TITLE     Antibiotic resistant Enterobacteriaceae from E-waste dumpsites,
            Nigeria
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7483)
  AUTHORS   Ikhimiukor,O., Vollmers,J., Adeleke,R.A., Kaster,A.-K.,
            Mueller,J.A. and Adelowo,O.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-APR-2020) Department of Environmental Biotechnology,
            University of Ibadan, Nigeria, Agbowo, Ibadan, Oyo State 200218,
            Nigeria
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            VDBG01000077.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Assembly-Data-START##
            Assembly Method        :: SPAdes v. 3.13.0
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 137.557114625718x
            Sequencing Technology  :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_019583735.1-RS_2024_11_20
            Annotation Date                   :: 11/20/2024 00:13:01
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,993
            CDSs (total)                      :: 4,869
            Genes (coding)                    :: 4,564
            CDSs (with protein)               :: 4,564
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 9, 15 (5S, 16S, 23S)
            complete rRNAs                    :: 3 (5S)
            partial rRNAs                     :: 5, 9, 15 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 77 of 305
            Pseudo Genes (incomplete)         :: 229 of 305
            Pseudo Genes (internal stop)      :: 35 of 305
            Pseudo Genes (multiple problems)  :: 34 of 305
            Pseudo Genes (short protein)      :: 1 of 305
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..7483
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="EC80_77"
                     /strain="EC_80"
                     /isolation_source="water from electronic waste dumpsite"
                     /db_xref="taxon:562"
                     /geo_loc_name="Nigeria: Lagos"
                     /lat_lon="6.461 N 3.191 E"
                     /collection_date="2017-08-10"
                     /collected_by="Ikhimiukor Odion"
     gene            <1..95
                     /locus_tag="FHB95_RS23090"
                     /old_locus_tag="FHB95_22985"
                     /pseudo
     CDS             <1..95
                     /locus_tag="FHB95_RS23090"
                     /old_locus_tag="FHB95_22985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020324562.1"
                     /note="incomplete; too short partial abutting assembly
                     gap; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo
                     /codon_start=3
                     /transl_table=11
                     /product="IS6 family transposase"
     gene            135..1280
                     /locus_tag="FHB95_RS23095"
                     /old_locus_tag="FHB95_22990"
     CDS             135..1280
                     /locus_tag="FHB95_RS23095"
                     /old_locus_tag="FHB95_22990"
                     /inference="COORDINATES: protein motif:HMM:NF023401.5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="6-phospho-alpha-glucosidase"
                     /protein_id="WP_220414389.1"
                     /translation="MQQCQFVYTTDKETAFSDADFFFIQIRTGGLAMRELDEQIPLFY
                     GCVGQETCGAGGMAYGLRSIGDMITLVNDIRHFAPDAWILNYTNPAAIVAEALQREFP
                     HDNRILNICDMPAAIMVSYAQLLGCEIWDLVPEYFGLNHFGWFTKVRNREGVDLTAEL
                     KRIILEEGISAVDPEIADDPSWQATFKNMQTMLKDNPEYLPNTYLQYYLYPEKMVEKE
                     DIANTRARQVINGREKRVFSLNERIIAAGTTANEHLHADIHGRYMVRVAASLAYNRGE
                     TYLVIVPNDGAIPNIQNDAMVEVPAALTNDGPKRFAVGTIPTFQKALIEGQLGYEKLV
                     VDAWFSGDRQTLVNALTLNRTVVDVPKAQQIVDELLRVNGDYLPQFH"
     gene            1332..2888
                     /locus_tag="FHB95_RS23100"
                     /old_locus_tag="FHB95_22995"
     CDS             1332..2888
                     /locus_tag="FHB95_RS23100"
                     /old_locus_tag="FHB95_22995"
                     /EC_number="2.7.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004098811.1"
                     /GO_function="GO:0015144 - carbohydrate transmembrane
                     transporter activity [Evidence IEA]"
                     /GO_process="GO:0009401 - phosphoenolpyruvate-dependent
                     sugar phosphotransferase system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="alpha-glucoside-specific PTS transporter subunit
                     IIBC"
                     /protein_id="WP_004098811.1"
                     /translation="MKDIIQRFGAAMFVPVLLFPAAGMLLGLSVMLLNQDLFPWAVEG
                     SAWVKVSTILLQASLAVFKNMALVFAVGLPIALAKSASGRAVLATLVSYITFNYVIGG
                     ILQFWGPELGVNYVEGERGLTDVGGILTLDTNLLGAIVIASLSVWVHNRFFDKKLPNW
                     AAVFGGTPLVVIVSFPIIVLMAIITCFTWPSIQHGINNLQTFLVGAGSFGVWMFTFLE
                     RIMIPTGLHHFVYGPVFYGPVAVDGGTVAHWIQNIQNFASNPAPLTEQFPQGGLMLTG
                     MGKVFGCTGIAMALYATAKPENKKMVLGLVLGAALTAILTGITEPIEFTFLFIAPALF
                     ALHAVLAATMATIAYWFGVSGNFQTGLIDFIFQNWLPLGSLHGDTYIVQVLIGLSFTA
                     IYFVVFRALIVKFDIPTPGRGSAEAKLYTKADYKGAQQNDSSSGVIDGGQASAFIEGL
                     GGKDNIALLTNCATRLRIKVHEPEKVAETQYFQEHGAVNMVRNGDSFQIIVGLTVPQV
                     REEMTQLIRA"
     gene            2960..>3241
                     /locus_tag="FHB95_RS23105"
                     /old_locus_tag="FHB95_23000"
                     /pseudo
     CDS             2960..>3241
                     /locus_tag="FHB95_RS23105"
                     /old_locus_tag="FHB95_23000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012472779.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS26 family transposase"
     gene            complement(<3241..>3429)
                     /locus_tag="FHB95_RS24870"
                     /old_locus_tag="FHB95_23005"
                     /pseudo
     CDS             complement(<3241..>3429)
                     /locus_tag="FHB95_RS24870"
                     /old_locus_tag="FHB95_23005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000008826.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3 family transposase"
     gene            complement(3683..4960)
                     /locus_tag="FHB95_RS23115"
                     /old_locus_tag="FHB95_23010"
     CDS             complement(3683..4960)
                     /locus_tag="FHB95_RS23115"
                     /old_locus_tag="FHB95_23010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016239947.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2254 domain-containing protein"
                     /protein_id="WP_045890830.1"
                     /translation="MISRWQWILRQTLKKLWFRATLFAMVAIITALLSILFRSMIPES
                     VSVKVGAEAVDNILNILASSMLAVTTFSLSIMVTAYGSATTNVTPRATRLVVEDVTTQ
                     NVLATFIGSFLFSLVGIIALNMGAYGERGRVILFIVTLVVIALIIITLLRWIQHLTSL
                     GRVGETTAKVEQAAIETFIARAKSPCLGGYPWLENNEQPKGTVAVYPEKIGYVEYIDM
                     VKLGSLLSNDPRHVYLVAQPGSFIHPSMPVLYLSSGQESSICTDLLETIIVSDVRSFA
                     QDPRFCLSVMAEIACRALSPAVNDPGTAIDVIGRGVRILSAYAQNKIDETEVIYPSVH
                     VAPLQIKDLLEDFFLPVARDGASMREIQIRVLKGLSMLSKGWPGMFAEAAHILASETL
                     EHATRTGHIAHDEYLIKSIYYNLFSGENPNKKP"
     gene            complement(5024..7021)
                     /locus_tag="FHB95_RS23120"
                     /old_locus_tag="FHB95_23015"
     CDS             complement(5024..7021)
                     /locus_tag="FHB95_RS23120"
                     /old_locus_tag="FHB95_23015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004119118.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="BCCT family transporter"
                     /protein_id="WP_008325030.1"
                     /translation="MSENDTIQKKSKSQINKAVFFTSALLIFLLVAFAAVFPDVADKN
                     FKLLQQQIFTNASWFYILAVALILLSVSFLGLSRYGDIKLGPDHAQPDFSYHSWFAML
                     FSAGMGIGLMFFGVAEPVMHYLSPPVGTPETVAAAKEAMRLTFFHWGLHAWAIYAIVA
                     LILAFFSYRHGLPLTLRSALYPIIGERIYGPVGHAVDIFAVIGTVFGVATSLGYGVLQ
                     VNAGLNHLFGVPINETVQVILIVVITGLATISVVSGLDKGIRILSELNLGLAVLLLAL
                     VLCLGPTVLLLKSFVENTGGYLSELVSKTFNLYAYEPKSSNWLGGWTLLYWGWWLSWS
                     PFVGMFIARVSRGRTIREFVTGVLFVPAGFTLMWMTVFGNSAIYLIMHQGAADLANTV
                     QQDVALALFNFLEHFPFSSVLSFIAMAMVIVFFVTSADSGAMVVDTLASGGVANTPVW
                     QRIFWASLIGIVAIALLIAGGLSALQTVTIASALPFSVILLISIYGLLKALRRDLTKR
                     ESLSMATIAPTAARNPIPWQRRLRNIAYLPKRSLVKRFMGDVIQPAMTLVQEELNKQG
                     TISHISDTDDERIRLEVDLGNELNFIYEVRLRGYNSPAFAMAAMDNDEQQAEQHRYYR
                     AEVYLKEGGQNYDVMGWNQEQLINDILDQYEKHLHFLHLVR"
CONTIG      join(VDBG01000077.1:1..7483)
//
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